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12
doc/_sources/fix.txt
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@ -170,8 +170,10 @@ of :ref:`this page <cmd_5>`.
* :doc:`adapt <fix_adapt>` - change a simulation parameter over time
* :doc:`addforce <fix_addforce>` - add a force to each atom
* :doc:`append/atoms <fix_append_atoms>` - append atoms to a running simulation
* :doc:`atom/swap <fix_atom_swap>` - Monte Carlo atom type swapping
* :doc:`aveforce <fix_aveforce>` - add an averaged force to each atom
* :doc:`ave/atom <fix_ave_atom>` - compute per-atom time-averaged quantities
* :doc:`ave/chunk <fix_ave_chunk>` - compute per-chunk time-averaged quantities
* :doc:`ave/correlate <fix_ave_correlate>` - compute/output time correlations
* :doc:`ave/histo <fix_ave_histo>` - compute/output time-averaged histograms
* :doc:`ave/spatial <fix_ave_spatial>` - compute/output time-averaged per-atom quantities by layer
@ -221,6 +223,7 @@ of :ref:`this page <cmd_5>`.
* :doc:`nvt/asphere <fix_nvt_asphere>` - NVT for aspherical particles
* :doc:`nvt/sllod <fix_nvt_sllod>` - NVT for NEMD with SLLOD equations
* :doc:`nvt/sphere <fix_nvt_sphere>` - NVT for spherical particles
* :doc:`oneway <fix_oneway>` - constrain particles on move in one direction
* :doc:`orient/fcc <fix_orient_fcc>` - add grain boundary migration force
* :doc:`planeforce <fix_planeforce>` - constrain atoms to move in a plane
* :doc:`poems <fix_poems>` - constrain clusters of atoms to move as coupled rigid bodies
@ -228,7 +231,7 @@ of :ref:`this page <cmd_5>`.
* :doc:`press/berendsen <fix_press_berendsen>` - pressure control by Berendsen barostat
* :doc:`print <fix_print>` - print text and variables during a simulation
* :doc:`property/atom <fix_property_atom>` - add customized per-atom values
* :doc:`qeq/comb <fix_qeq_comb>` - charge equilibration for COMB potential :doc:`qeq/dynamic <fix_qeq>` - charge equilibration via dynamic method :doc:`qeq/point <fix_qeq>` - charge equilibration via point method :doc:`qeq/shielded <fix_qeq>` - charge equilibration via shielded method :doc:`qeq/slater <fix_qeq>` - charge equilibration via Slater method :doc:`reax/bonds <fix_reax_bonds>` - write out ReaxFF bond information :doc:`recenter <fix_recenter>` - constrain the center-of-mass position of a group of atoms
* :doc:`qeq/comb <fix_qeq_comb>` - charge equilibration for COMB potential :doc:`qeq/dynamic <fix_qeq>` - charge equilibration via dynamic method :doc:`qeq/fire <fix_qeq>` - charge equilibration via FIRE minimizer :doc:`qeq/point <fix_qeq>` - charge equilibration via point method :doc:`qeq/shielded <fix_qeq>` - charge equilibration via shielded method :doc:`qeq/slater <fix_qeq>` - charge equilibration via Slater method :doc:`reax/bonds <fix_reax_bonds>` - write out ReaxFF bond information :doc:`recenter <fix_recenter>` - constrain the center-of-mass position of a group of atoms
* :doc:`restrain <fix_restrain>` - constrain a bond, angle, dihedral
* :doc:`rigid <fix_rigid>` - constrain one or more clusters of atoms to move as a rigid body with NVE integration
* :doc:`rigid/nph <fix_rigid>` - constrain one or more clusters of atoms to move as a rigid body with NPH integration
@ -236,6 +239,10 @@ of :ref:`this page <cmd_5>`.
* :doc:`rigid/nve <fix_rigid>` - constrain one or more clusters of atoms to move as a rigid body with alternate NVE integration
* :doc:`rigid/nvt <fix_rigid>` - constrain one or more clusters of atoms to move as a rigid body with NVT integration
* :doc:`rigid/small <fix_rigid>` - constrain many small clusters of atoms to move as a rigid body with NVE integration
* :doc:`rigid/small/nph <fix_rigid>` - constrain many small clusters of atoms to move as a rigid body with NPH integration
* :doc:`rigid/small/npt <fix_rigid>` - constrain many small clusters of atoms to move as a rigid body with NPT integration
* :doc:`rigid/small/nve <fix_rigid>` - constrain many small clusters of atoms to move as a rigid body with alternate NVE integration
* :doc:`rigid/small/nvt <fix_rigid>` - constrain many small clusters of atoms to move as a rigid body with NVT integration
* :doc:`setforce <fix_setforce>` - set the force on each atom
* :doc:`shake <fix_shake>` - SHAKE constraints on bonds and/or angles
* :doc:`spring <fix_spring>` - apply harmonic spring force to group of atoms
@ -245,7 +252,10 @@ of :ref:`this page <cmd_5>`.
* :doc:`store/force <fix_store_force>` - store force on each atom
* :doc:`store/state <fix_store_state>` - store attributes for each atom
* :doc:`temp/berendsen <fix_temp_berendsen>` - temperature control by Berendsen thermostat
* :doc:`temp/csld <fix_temp_csvr>` - canonical sampling thermostat with Langevin dynamics
* :doc:`temp/csvr <fix_temp_csvr>` - canonical sampling thermostat with Hamiltonian dynamics
* :doc:`temp/rescale <fix_temp_rescale>` - temperature control by velocity rescaling
* :doc:`tfmc <fix_tfmc>` - perform force-bias Monte Carlo with time-stamped method
* :doc:`thermal/conductivity <fix_thermal_conductivity>` - Muller-Plathe kinetic energy exchange for thermal conductivity calculation
* :doc:`tmd <fix_tmd>` - guide a group of atoms to a new configuration
* :doc:`ttm <fix_ttm>` - two-temperature model for electronic/atomic coupling

2
doc/_sources/pair_style.txt
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@ -155,11 +155,13 @@ in the pair section of :ref:`this page <cmd_5>`.
* :doc:`pair_style lj/class2 <pair_class2>` - COMPASS (class 2) force field with no Coulomb
* :doc:`pair_style lj/class2/coul/cut <pair_class2>` - COMPASS with cutoff Coulomb
* :doc:`pair_style lj/class2/coul/long <pair_class2>` - COMPASS with long-range Coulomb
* :doc:`pair_style lj/cubic <pair_lj_cubic>` - LJ with cubic after inflection point
* :doc:`pair_style lj/cut <pair_lj>` - cutoff Lennard-Jones potential with no Coulomb
* :doc:`pair_style lj/cut/coul/cut <pair_lj>` - LJ with cutoff Coulomb
* :doc:`pair_style lj/cut/coul/debye <pair_lj>` - LJ with Debye screening added to Coulomb
* :doc:`pair_style lj/cut/coul/dsf <pair_lj>` - LJ with Coulombics via damped shifted forces
* :doc:`pair_style lj/cut/coul/long <pair_lj>` - LJ with long-range Coulombics
* :doc:`pair_style lj/cut/coul/long/cs <pair_lj>` - LJ with long-range Coulombics and core/shell
* :doc:`pair_style lj/cut/coul/msm <pair_lj>` - LJ with long-range MSM Coulombics
* :doc:`pair_style lj/cut/dipole/cut <pair_dipole>` - point dipoles with cutoff
* :doc:`pair_style lj/cut/dipole/long <pair_dipole>` - point dipoles with long-range Ewald

23
doc/_sources/run_style.txt
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@ -43,10 +43,10 @@ Syntax
cut2 = outer cutoff between pair middle and pair outer (distance units)
*outer* value = M
M = which level (1-N) to compute pair outer forces in
*hybrid* values = M1 [M2 ...] (as many values as there are hybrid sub-styles
*hybrid* values = M1 M2 ... (as many values as there are hybrid sub-styles
M1 = which level (1-N) to compute the first pair_style hybrid sub-style in
M2 = which level (1-N) to compute the second pair_style hybrid sub-style in
...
M3,etc
*kspace* value = M
M = which level (1-N) to compute kspace forces in
@ -185,15 +185,16 @@ with that pair style, meaning all pairwise forces are computed at the
same rRESPA level. See the doc pages for individual pair styles for
details.i
Another variant to use pair potentials in rRESPA is with the *hybrid*
keyword, which requires the use of a :doc:`hybrid pair_style <pair_hybrid>`
In this scenario, different sub-styles of the hybrid pair style are
evaluated at different rRESPA levels. Thus the hybrid keyword requires
as many level assignments as there are hybrid substyles which designate
the respective sub-styles to the rRESPA level according to their order
of definition in the pair_style command. Since the *hybrid* designates
pair force computations, it is mututally exclusive with either the *pair*
or the *inner*/*middle*/*outer* keywords.
Another option for using pair potentials with rRESPA is with the
*hybrid* keyword, which requires the use of the :doc:`pair_style hybrid or hybrid/overlay <pair_hybrid>` command. In this scenario, different
sub-styles of the hybrid pair style are evaluated at different rRESPA
levels. This can be useful, for example, to set different timesteps
for hybrid coarse-grained/all-atom models. The *hybrid* keyword
requires as many level assignments as there are hybrid substyles,
which assigns each sub-style to a rRESPA level, following their order
of definition in the pair_style command. Since the *hybrid* keyword
operates on pair style computations, it is mututally exclusive with
either the *pair* or the *inner*/*middle*/*outer* keywords.
When using rRESPA (or for any MD simulation) care must be taken to
choose a timestep size(s) that insures the Hamiltonian for the chosen

12
doc/fix.html
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@ -276,8 +276,10 @@ of <a class="reference internal" href="Section_commands.html#cmd-5"><span>this p
<li><a class="reference internal" href="fix_adapt.html"><em>adapt</em></a> - change a simulation parameter over time</li>
<li><a class="reference internal" href="fix_addforce.html"><em>addforce</em></a> - add a force to each atom</li>
<li><a class="reference internal" href="fix_append_atoms.html"><em>append/atoms</em></a> - append atoms to a running simulation</li>
<li><a class="reference internal" href="fix_atom_swap.html"><em>atom/swap</em></a> - Monte Carlo atom type swapping</li>
<li><a class="reference internal" href="fix_aveforce.html"><em>aveforce</em></a> - add an averaged force to each atom</li>
<li><a class="reference internal" href="fix_ave_atom.html"><em>ave/atom</em></a> - compute per-atom time-averaged quantities</li>
<li><a class="reference internal" href="fix_ave_chunk.html"><em>ave/chunk</em></a> - compute per-chunk time-averaged quantities</li>
<li><a class="reference internal" href="fix_ave_correlate.html"><em>ave/correlate</em></a> - compute/output time correlations</li>
<li><a class="reference internal" href="fix_ave_histo.html"><em>ave/histo</em></a> - compute/output time-averaged histograms</li>
<li><a class="reference internal" href="fix_ave_spatial.html"><em>ave/spatial</em></a> - compute/output time-averaged per-atom quantities by layer</li>
@ -327,6 +329,7 @@ of <a class="reference internal" href="Section_commands.html#cmd-5"><span>this p
<li><a class="reference internal" href="fix_nvt_asphere.html"><em>nvt/asphere</em></a> - NVT for aspherical particles</li>
<li><a class="reference internal" href="fix_nvt_sllod.html"><em>nvt/sllod</em></a> - NVT for NEMD with SLLOD equations</li>
<li><a class="reference internal" href="fix_nvt_sphere.html"><em>nvt/sphere</em></a> - NVT for spherical particles</li>
<li><a class="reference internal" href="fix_oneway.html"><em>oneway</em></a> - constrain particles on move in one direction</li>
<li><a class="reference internal" href="fix_orient_fcc.html"><em>orient/fcc</em></a> - add grain boundary migration force</li>
<li><a class="reference internal" href="fix_planeforce.html"><em>planeforce</em></a> - constrain atoms to move in a plane</li>
<li><a class="reference internal" href="fix_poems.html"><em>poems</em></a> - constrain clusters of atoms to move as coupled rigid bodies</li>
@ -334,7 +337,7 @@ of <a class="reference internal" href="Section_commands.html#cmd-5"><span>this p
<li><a class="reference internal" href="fix_press_berendsen.html"><em>press/berendsen</em></a> - pressure control by Berendsen barostat</li>
<li><a class="reference internal" href="fix_print.html"><em>print</em></a> - print text and variables during a simulation</li>
<li><a class="reference internal" href="fix_property_atom.html"><em>property/atom</em></a> - add customized per-atom values</li>
<li><a class="reference internal" href="fix_qeq_comb.html"><em>qeq/comb</em></a> - charge equilibration for COMB potential <a class="reference internal" href="fix_qeq.html"><em>qeq/dynamic</em></a> - charge equilibration via dynamic method <a class="reference internal" href="fix_qeq.html"><em>qeq/point</em></a> - charge equilibration via point method <a class="reference internal" href="fix_qeq.html"><em>qeq/shielded</em></a> - charge equilibration via shielded method <a class="reference internal" href="fix_qeq.html"><em>qeq/slater</em></a> - charge equilibration via Slater method <a class="reference internal" href="fix_reax_bonds.html"><em>reax/bonds</em></a> - write out ReaxFF bond information <a class="reference internal" href="fix_recenter.html"><em>recenter</em></a> - constrain the center-of-mass position of a group of atoms</li>
<li><a class="reference internal" href="fix_qeq_comb.html"><em>qeq/comb</em></a> - charge equilibration for COMB potential <a class="reference internal" href="fix_qeq.html"><em>qeq/dynamic</em></a> - charge equilibration via dynamic method <a class="reference internal" href="fix_qeq.html"><em>qeq/fire</em></a> - charge equilibration via FIRE minimizer <a class="reference internal" href="fix_qeq.html"><em>qeq/point</em></a> - charge equilibration via point method <a class="reference internal" href="fix_qeq.html"><em>qeq/shielded</em></a> - charge equilibration via shielded method <a class="reference internal" href="fix_qeq.html"><em>qeq/slater</em></a> - charge equilibration via Slater method <a class="reference internal" href="fix_reax_bonds.html"><em>reax/bonds</em></a> - write out ReaxFF bond information <a class="reference internal" href="fix_recenter.html"><em>recenter</em></a> - constrain the center-of-mass position of a group of atoms</li>
<li><a class="reference internal" href="fix_restrain.html"><em>restrain</em></a> - constrain a bond, angle, dihedral</li>
<li><a class="reference internal" href="fix_rigid.html"><em>rigid</em></a> - constrain one or more clusters of atoms to move as a rigid body with NVE integration</li>
<li><a class="reference internal" href="fix_rigid.html"><em>rigid/nph</em></a> - constrain one or more clusters of atoms to move as a rigid body with NPH integration</li>
@ -342,6 +345,10 @@ of <a class="reference internal" href="Section_commands.html#cmd-5"><span>this p
<li><a class="reference internal" href="fix_rigid.html"><em>rigid/nve</em></a> - constrain one or more clusters of atoms to move as a rigid body with alternate NVE integration</li>
<li><a class="reference internal" href="fix_rigid.html"><em>rigid/nvt</em></a> - constrain one or more clusters of atoms to move as a rigid body with NVT integration</li>
<li><a class="reference internal" href="fix_rigid.html"><em>rigid/small</em></a> - constrain many small clusters of atoms to move as a rigid body with NVE integration</li>
<li><a class="reference internal" href="fix_rigid.html"><em>rigid/small/nph</em></a> - constrain many small clusters of atoms to move as a rigid body with NPH integration</li>
<li><a class="reference internal" href="fix_rigid.html"><em>rigid/small/npt</em></a> - constrain many small clusters of atoms to move as a rigid body with NPT integration</li>
<li><a class="reference internal" href="fix_rigid.html"><em>rigid/small/nve</em></a> - constrain many small clusters of atoms to move as a rigid body with alternate NVE integration</li>
<li><a class="reference internal" href="fix_rigid.html"><em>rigid/small/nvt</em></a> - constrain many small clusters of atoms to move as a rigid body with NVT integration</li>
<li><a class="reference internal" href="fix_setforce.html"><em>setforce</em></a> - set the force on each atom</li>
<li><a class="reference internal" href="fix_shake.html"><em>shake</em></a> - SHAKE constraints on bonds and/or angles</li>
<li><a class="reference internal" href="fix_spring.html"><em>spring</em></a> - apply harmonic spring force to group of atoms</li>
@ -351,7 +358,10 @@ of <a class="reference internal" href="Section_commands.html#cmd-5"><span>this p
<li><a class="reference internal" href="fix_store_force.html"><em>store/force</em></a> - store force on each atom</li>
<li><a class="reference internal" href="fix_store_state.html"><em>store/state</em></a> - store attributes for each atom</li>
<li><a class="reference internal" href="fix_temp_berendsen.html"><em>temp/berendsen</em></a> - temperature control by Berendsen thermostat</li>
<li><a class="reference internal" href="fix_temp_csvr.html"><em>temp/csld</em></a> - canonical sampling thermostat with Langevin dynamics</li>
<li><a class="reference internal" href="fix_temp_csvr.html"><em>temp/csvr</em></a> - canonical sampling thermostat with Hamiltonian dynamics</li>
<li><a class="reference internal" href="fix_temp_rescale.html"><em>temp/rescale</em></a> - temperature control by velocity rescaling</li>
<li><a class="reference internal" href="fix_tfmc.html"><em>tfmc</em></a> - perform force-bias Monte Carlo with time-stamped method</li>
<li><a class="reference internal" href="fix_thermal_conductivity.html"><em>thermal/conductivity</em></a> - Muller-Plathe kinetic energy exchange for thermal conductivity calculation</li>
<li><a class="reference internal" href="fix_tmd.html"><em>tmd</em></a> - guide a group of atoms to a new configuration</li>
<li><a class="reference internal" href="fix_ttm.html"><em>ttm</em></a> - two-temperature model for electronic/atomic coupling</li>

15
doc/fix.txt
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@ -165,8 +165,10 @@ of "this page"_Section_commands.html#cmd_5.
"adapt"_fix_adapt.html - change a simulation parameter over time
"addforce"_fix_addforce.html - add a force to each atom
"append/atoms"_fix_append_atoms.html - append atoms to a running simulation
"atom/swap"_fix_atom_swap.html - Monte Carlo atom type swapping
"aveforce"_fix_aveforce.html - add an averaged force to each atom
"ave/atom"_fix_ave_atom.html - compute per-atom time-averaged quantities
"ave/chunk"_fix_ave_chunk.html - compute per-chunk time-averaged quantities
"ave/correlate"_fix_ave_correlate.html - compute/output time correlations
"ave/histo"_fix_ave_histo.html - compute/output time-averaged histograms
"ave/spatial"_fix_ave_spatial.html - compute/output time-averaged per-atom quantities by layer
@ -216,6 +218,7 @@ of "this page"_Section_commands.html#cmd_5.
"nvt/asphere"_fix_nvt_asphere.html - NVT for aspherical particles
"nvt/sllod"_fix_nvt_sllod.html - NVT for NEMD with SLLOD equations
"nvt/sphere"_fix_nvt_sphere.html - NVT for spherical particles
"oneway"_fix_oneway.html - constrain particles on move in one direction
"orient/fcc"_fix_orient_fcc.html - add grain boundary migration force
"planeforce"_fix_planeforce.html - constrain atoms to move in a plane
"poems"_fix_poems.html - constrain clusters of atoms to move \
@ -227,6 +230,7 @@ of "this page"_Section_commands.html#cmd_5.
"property/atom"_fix_property_atom.html - add customized per-atom values
"qeq/comb"_fix_qeq_comb.html - charge equilibration for COMB potential \
"qeq/dynamic"_fix_qeq.html - charge equilibration via dynamic method \
"qeq/fire"_fix_qeq.html - charge equilibration via FIRE minimizer \
"qeq/point"_fix_qeq.html - charge equilibration via point method \
"qeq/shielded"_fix_qeq.html - charge equilibration via shielded method \
"qeq/slater"_fix_qeq.html - charge equilibration via Slater method \
@ -246,6 +250,14 @@ of "this page"_Section_commands.html#cmd_5.
move as a rigid body with NVT integration
"rigid/small"_fix_rigid.html - constrain many small clusters of atoms to \
move as a rigid body with NVE integration
"rigid/small/nph"_fix_rigid.html - constrain many small clusters of atoms to \
move as a rigid body with NPH integration
"rigid/small/npt"_fix_rigid.html - constrain many small clusters of atoms to \
move as a rigid body with NPT integration
"rigid/small/nve"_fix_rigid.html - constrain many small clusters of atoms to \
move as a rigid body with alternate NVE integration
"rigid/small/nvt"_fix_rigid.html - constrain many small clusters of atoms to \
move as a rigid body with NVT integration
"setforce"_fix_setforce.html - set the force on each atom
"shake"_fix_shake.html - SHAKE constraints on bonds and/or angles
"spring"_fix_spring.html - apply harmonic spring force to group of atoms
@ -257,8 +269,11 @@ of "this page"_Section_commands.html#cmd_5.
"store/state"_fix_store_state.html - store attributes for each atom
"temp/berendsen"_fix_temp_berendsen.html - temperature control by \
Berendsen thermostat
"temp/csld"_fix_temp_csvr.html - canonical sampling thermostat with Langevin dynamics
"temp/csvr"_fix_temp_csvr.html - canonical sampling thermostat with Hamiltonian dynamics
"temp/rescale"_fix_temp_rescale.html - temperature control by \
velocity rescaling
"tfmc"_fix_tfmc.html - perform force-bias Monte Carlo with time-stamped method
"thermal/conductivity"_fix_thermal_conductivity.html - Muller-Plathe kinetic energy exchange for \
thermal conductivity calculation
"tmd"_fix_tmd.html - guide a group of atoms to a new configuration

2
doc/pair_style.html
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@ -261,11 +261,13 @@ in the pair section of <a class="reference internal" href="Section_commands.html
<li><a class="reference internal" href="pair_class2.html"><em>pair_style lj/class2</em></a> - COMPASS (class 2) force field with no Coulomb</li>
<li><a class="reference internal" href="pair_class2.html"><em>pair_style lj/class2/coul/cut</em></a> - COMPASS with cutoff Coulomb</li>
<li><a class="reference internal" href="pair_class2.html"><em>pair_style lj/class2/coul/long</em></a> - COMPASS with long-range Coulomb</li>
<li><a class="reference internal" href="pair_lj_cubic.html"><em>pair_style lj/cubic</em></a> - LJ with cubic after inflection point</li>
<li><a class="reference internal" href="pair_lj.html"><em>pair_style lj/cut</em></a> - cutoff Lennard-Jones potential with no Coulomb</li>
<li><a class="reference internal" href="pair_lj.html"><em>pair_style lj/cut/coul/cut</em></a> - LJ with cutoff Coulomb</li>
<li><a class="reference internal" href="pair_lj.html"><em>pair_style lj/cut/coul/debye</em></a> - LJ with Debye screening added to Coulomb</li>
<li><a class="reference internal" href="pair_lj.html"><em>pair_style lj/cut/coul/dsf</em></a> - LJ with Coulombics via damped shifted forces</li>
<li><a class="reference internal" href="pair_lj.html"><em>pair_style lj/cut/coul/long</em></a> - LJ with long-range Coulombics</li>
<li><a class="reference internal" href="pair_lj.html"><em>pair_style lj/cut/coul/long/cs</em></a> - LJ with long-range Coulombics and core/shell</li>
<li><a class="reference internal" href="pair_lj.html"><em>pair_style lj/cut/coul/msm</em></a> - LJ with long-range MSM Coulombics</li>
<li><a class="reference internal" href="pair_dipole.html"><em>pair_style lj/cut/dipole/cut</em></a> - point dipoles with cutoff</li>
<li><a class="reference internal" href="pair_dipole.html"><em>pair_style lj/cut/dipole/long</em></a> - point dipoles with long-range Ewald</li>

2
doc/pair_style.txt
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@ -152,11 +152,13 @@ in the pair section of "this page"_Section_commands.html#cmd_5.
"pair_style lj/class2"_pair_class2.html - COMPASS (class 2) force field with no Coulomb
"pair_style lj/class2/coul/cut"_pair_class2.html - COMPASS with cutoff Coulomb
"pair_style lj/class2/coul/long"_pair_class2.html - COMPASS with long-range Coulomb
"pair_style lj/cubic"_pair_lj_cubic.html - LJ with cubic after inflection point
"pair_style lj/cut"_pair_lj.html - cutoff Lennard-Jones potential with no Coulomb
"pair_style lj/cut/coul/cut"_pair_lj.html - LJ with cutoff Coulomb
"pair_style lj/cut/coul/debye"_pair_lj.html - LJ with Debye screening added to Coulomb
"pair_style lj/cut/coul/dsf"_pair_lj.html - LJ with Coulombics via damped shifted forces
"pair_style lj/cut/coul/long"_pair_lj.html - LJ with long-range Coulombics
"pair_style lj/cut/coul/long/cs"_pair_lj.html - LJ with long-range Coulombics and core/shell
"pair_style lj/cut/coul/msm"_pair_lj.html - LJ with long-range MSM Coulombics
"pair_style lj/cut/dipole/cut"_pair_dipole.html - point dipoles with cutoff
"pair_style lj/cut/dipole/long"_pair_dipole.html - point dipoles with long-range Ewald

23
doc/run_style.html
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@ -165,10 +165,10 @@
cut2 = outer cutoff between pair middle and pair outer (distance units)
<em>outer</em> value = M
M = which level (1-N) to compute pair outer forces in
<em>hybrid</em> values = M1 [M2 ...] (as many values as there are hybrid sub-styles
<em>hybrid</em> values = M1 M2 ... (as many values as there are hybrid sub-styles
M1 = which level (1-N) to compute the first pair_style hybrid sub-style in
M2 = which level (1-N) to compute the second pair_style hybrid sub-style in
...
M3,etc
<em>kspace</em> value = M
M = which level (1-N) to compute kspace forces in
</pre>
@ -280,15 +280,16 @@ and <em>outer</em> keywords. If not, only the <em>pair</em> keyword can be used
with that pair style, meaning all pairwise forces are computed at the
same rRESPA level. See the doc pages for individual pair styles for
details.i</p>
<p>Another variant to use pair potentials in rRESPA is with the <em>hybrid</em>
keyword, which requires the use of a <a class="reference internal" href="pair_hybrid.html"><em>hybrid pair_style</em></a>
In this scenario, different sub-styles of the hybrid pair style are
evaluated at different rRESPA levels. Thus the hybrid keyword requires
as many level assignments as there are hybrid substyles which designate
the respective sub-styles to the rRESPA level according to their order
of definition in the pair_style command. Since the <em>hybrid</em> designates
pair force computations, it is mututally exclusive with either the <em>pair</em>
or the <em>inner</em>/<em>middle</em>/<em>outer</em> keywords.</p>
<p>Another option for using pair potentials with rRESPA is with the
<em>hybrid</em> keyword, which requires the use of the <a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid or hybrid/overlay</em></a> command. In this scenario, different
sub-styles of the hybrid pair style are evaluated at different rRESPA
levels. This can be useful, for example, to set different timesteps
for hybrid coarse-grained/all-atom models. The <em>hybrid</em> keyword
requires as many level assignments as there are hybrid substyles,
which assigns each sub-style to a rRESPA level, following their order
of definition in the pair_style command. Since the <em>hybrid</em> keyword
operates on pair style computations, it is mututally exclusive with
either the <em>pair</em> or the <em>inner</em>/<em>middle</em>/<em>outer</em> keywords.</p>
<p>When using rRESPA (or for any MD simulation) care must be taken to
choose a timestep size(s) that insures the Hamiltonian for the chosen
ensemble is conserved. For the constant NVE ensemble, total energy

24
doc/run_style.txt
View File

@ -43,10 +43,10 @@ style = {verlet} or {verlet/split} or {respa} or {respa/omp} :ulb,l
cut2 = outer cutoff between pair middle and pair outer (distance units)
{outer} value = M
M = which level (1-N) to compute pair outer forces in
{hybrid} values = M1 \[M2 ...\] (as many values as there are hybrid sub-styles
{hybrid} values = M1 M2 ... (as many values as there are hybrid sub-styles
M1 = which level (1-N) to compute the first pair_style hybrid sub-style in
M2 = which level (1-N) to compute the second pair_style hybrid sub-style in
...
M3,etc
{kspace} value = M
M = which level (1-N) to compute kspace forces in :pre
:ule
@ -170,15 +170,17 @@ with that pair style, meaning all pairwise forces are computed at the
same rRESPA level. See the doc pages for individual pair styles for
details.i
Another variant to use pair potentials in rRESPA is with the {hybrid}
keyword, which requires the use of a "hybrid pair_style"_pair_hybrid.html
In this scenario, different sub-styles of the hybrid pair style are
evaluated at different rRESPA levels. Thus the hybrid keyword requires
as many level assignments as there are hybrid substyles which designate
the respective sub-styles to the rRESPA level according to their order
of definition in the pair_style command. Since the {hybrid} designates
pair force computations, it is mututally exclusive with either the {pair}
or the {inner}/{middle}/{outer} keywords.
Another option for using pair potentials with rRESPA is with the
{hybrid} keyword, which requires the use of the "pair_style hybrid or
hybrid/overlay"_pair_hybrid.html command. In this scenario, different
sub-styles of the hybrid pair style are evaluated at different rRESPA
levels. This can be useful, for example, to set different timesteps
for hybrid coarse-grained/all-atom models. The {hybrid} keyword
requires as many level assignments as there are hybrid substyles,
which assigns each sub-style to a rRESPA level, following their order
of definition in the pair_style command. Since the {hybrid} keyword
operates on pair style computations, it is mututally exclusive with
either the {pair} or the {inner}/{middle}/{outer} keywords.
When using rRESPA (or for any MD simulation) care must be taken to
choose a timestep size(s) that insures the Hamiltonian for the chosen

2
doc/searchindex.js
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